dynwrap (version 1.2.1)

add_cell_graph: Constructs a trajectory using a graph between cells, by mapping cells onto a set of backbone cells.

Description

The cells that are part of the backbone will form the trajectory. All other cells are moved towards the nearest cell that is part of the backbone.

Usage

add_cell_graph(
  dataset,
  cell_graph,
  to_keep,
  milestone_prefix = "milestone_",
  ...
)

Arguments

dataset

A dataset created by wrap_data() or wrap_expression()

cell_graph

The edges between cells, a dataframe containing the from and to cells, the *length, and whether this edge is directed

to_keep

Whether a cells is part of the backbone. May be a character vector with the identifiers of the backbone cells, or a named boolean vector whether a cell is from the backbone

milestone_prefix

A prefix to add to the id of the cell ids when they are used as milestones, in order to avoid any naming conflicts,

...

extra information to be stored in the wrapper.

Value

The dataset object with trajectory information, including:

• milestone_ids: The names of the milestones, a character vector.

• milestone_network: The network between the milestones, a dataframe with the from milestone, to milestone, length of the edge, and whether it is directed.

• divergence_regions: The regions between three or more milestones where cells are diverging, a dataframe with the divergence id (divergence_id), the milestone id (milestone_id) and whether this milestone is the start of the divergence (is_start)

• milestone_percentages: For each cell its closeness to a particular milestone, a dataframe with the cell id (cell_id), the milestone id (milestone_id), and its percentage (a number between 0 and 1 where higher values indicate that a cell is close to the milestone).

• progressions: For each cell its progression along a particular edge of the milestone_network. Contains the same information as milestone_percentages. A dataframe with cell id (cell_id), from milestone, to milestone, and its percentage (a number between 0 and 1 where higher values indicate that a cell is close to the to milestone and far from the from milestone).

Examples

# NOT RUN {
library(dplyr)
dataset <- wrap_data(cell_ids = letters)

backbone_cell_graph <- tibble::tibble(
  from = letters[1:10],
  to = letters[2:11],
  length = 1,
  directed = TRUE
)
leaves_cell_graph <- tibble::tibble(
  from = letters[12:26],
  to = sample(letters[1:11], 15, replace = TRUE),
  length = 1,
  directed = TRUE
)
cell_graph <- bind_rows(backbone_cell_graph, leaves_cell_graph)
cell_graph
to_keep <- letters[1:11]
to_keep

trajectory <- add_cell_graph(dataset, cell_graph, to_keep)

# for plotting the result, install dynplot
#- dynplot::plot_graph(trajectory)
# }